[gmx-users] rigid tetrahedral molecule

Sanku M msanku65 at yahoo.com
Thu Apr 28 03:12:50 CEST 2011

 I am interested in simulating a anionic molecule BF4(-)  ( Boron 
tetrafluoride).  In the paper which developed the parameters for this molecule, 
it is mentioned that it has been used as 'rigid' molecule i.e the molecule only 
has non-bonding interaction but there was no intramolecular motion as the 
geometry was fixed.
 I am trying to simulate this molecule in gromacs treating it as rigid.  But, I 
was looking for best way to 'rigidify' this molecule.

I was wondering whether using LINCS to constrain all B-F and F-F bonds will be 
good enough .  Or, Should I use virtual sites ? If I really need to use virtual 
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?

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